Hello,
I need help determining the EUR ancestry LD block for a single SNP for my project. PLINK does not seem to work with just one SNP.
Question 1: I found a paper that determines LD blocks by starting and ending from the most distant two SNPs with an LD score > 0.5 according to this paper: PMID: 35184600. Many previous papers have stated that LD blocks are <100 kb (for example, PMID: 18000525, DOI: 10.1038/sj.ejhg.5201953). Are there other methods to determine LD blocks from a single SNP?
Question 2: A recent preprint (https://www.biorxiv.org/content/10.1101/2022.03.04.483057v1.full.pdf) mentioned in this paper (Table 1) that the average hg38 LD block is around a million base pairs. What kind of block are they exactly determining in Table 1? I'm confused about what they are referring to.
Thank you in advance!
